Obstructive sleep apnoea (OSA) has been reported to be associated with brain hypotrophy and cognitive dysfunction; however, whether these normalise after treatment is unclear. The overall aim of this thesis is to investigate the relationship between OSA and brain structure using FreeSurfer (a new automated technique that reliably measures brain structures). I have investigated changes in brain morphology and the newly described phenomenon in OSA of ischaemic preconditioning. Chapters 4 and 5 will also assess brain structural response to CPAP, and investigate the association between brain structure and cognitive function in OSA. Chapter 3 reports an observational study investigating brain structure. FreeSurfer analysis of magnetic resonance imaging (MRI) found OSA patients had hypertrophy in the right hippocampus (p=0.03) and right choroid plexus (p=0.02) but hypotrophy of the corpus callosum (p=0.04) compared to healthy controls. Chapter 4 reports a randomised controlled trial of CPAP in OSA. At baseline hypotrophy was seen in the corpus callosum (p=0.03) and pallidum (p=0.03) of OSA patients compared to healthy controls. Hypertrophic changes in the right thalamus were seen in the CPAP group after 1 month (p=0.06), associated with improvement in verbal memory (p=0.04). Chapter 5 reports a randomised controlled trial of CPAP in older patients with OSA. A significant decrease in left fimbria volume was seen in the CPAP group (p=0.01). A significant increase in the left presubiculum volume was seen in the best supportive care group (p=0.03). No hippocampal hypertrophy was seen in the CPAP group. In summary, young and middle-aged OSA patients had evidence of brain hypotrophy, but also areas of hypertrophy that may signify dendritic sprouting and increased connectivity as a result of ischaemic preconditioning. This allows recovery of brain hypotrophy after CPAP treatment. This was not seen in older OSA patients suggesting an age-related difference which may have implications for OSA treatment in older people.